2YFI

Crystal Structure of Biphenyl dioxygenase variant RR41 (BPDO-RR41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Retuning Rieske-Type Oxygenases to Expand Substrate Range.

Mohammadi, M.Viger, J.Kumar, P.Barriault, D.Bolin, J.T.Sylvestre, M.

(2011) J Biol Chem 286: 27612

  • DOI: 10.1074/jbc.M111.255174
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. Bph ...

    Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE(LB400) showed that the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.


    Organizational Affiliation

    Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL DIOXYGENASE SUBUNIT ALPHA
A, C, E, G, I, K
459Paraburkholderia xenovorans LB400Mutation(s): 5 
Gene Names: bphABxeno_C1131Bxe_C1197
EC: 1.14.12.18
Find proteins for P37333 (Paraburkholderia xenovorans (strain LB400))
Go to UniProtKB:  P37333

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL DIOXYGENASE SUBUNIT BETA
B, D, F, H, J, L
188Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: bphEBxeno_C1130Bxe_C1196
EC: 1.14.12.18
Find proteins for P37334 (Paraburkholderia xenovorans (strain LB400))
Go to UniProtKB:  P37334
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download CCD File 
A, C, E, G, I, K
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, C, E, G, I, K
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.969α = 90
b = 277.808β = 117.61
c = 92.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-04-06 
  • Released Date: 2011-06-08 
  • Deposition Author(s): Kumar, P., Bolin, J.T.

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance